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\begin{document}

\input{title}

\myignore{
%some comments
Текст должен полностью  описывать вашу задачу и решение, а также ваш персональный вклад. По опыту обычно в тексте дипломной  работы не меньше 20-30 страниц (не считая приложений) и не больше 50, на 40 страницах можно раскрыть практически любую тему.

Рекомендованный план диплома обсуждался на встрече с Андреем Николаевичем, так что подробности я опускаю, привожу только примерное содержание:  введение, постановка задачи, обзор литературы (предметная область,  смежные работы, конкурирующие решения и т.п.), предлагаемое решение,  особенности реализации (архитектура, основные сложности и т.п.), апробация/внедрение, сравнения и соотнесения, результаты работы. 
}

\part{Introuduction}
\section{What is genome}
\section{Why do people need to ``decode'' genomes}
\section{What does the process look like}
\subsection{Sequencing}
\subsection{Assembling}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\part{Problem definition}
%Definitions, input data, aims of work

\section{Some definitions}
	

\myignore{
%todo not sure that we need this section

\section{Graph approaches}
\subsection{Hamiltonian, OLC}
\subsection{Euler}
\subsection{String graph}
}

\section{\dbg{}s}
\subsection{History, classical definition}
\subsection{\dbg of the ideal read set}
%What is ideal read set? How is the graph constructed? Generalization on multiple edges. Genome corresponds to some eulerian cycle in this graph. And how to read sequence along the graph.
\subsection{Why it doesn't work this way}
%All assumptions on the properties of read set are wrong (not all $k$-mers are reads, reads have mistakes, genome not cyclic, don't know muliplicities) + right cycle should be chosen with respect to information of paired reads, not single ones.
\subsection{\dbg on the real read set}
%we chose $k$-mers instead of whole reads to have connected graph. Have to forget about multiplicities (should write about chinese postman???). Because of mistakes have rubbish edges, so real genome walks not through all of them...

\subsection{Flavours of \dbg{}s}
%condensed graphs, reverse complement info maintaining

\subsection{Aims of work}
% full \dbg lifecycle, usable interfaces, scalable and clear architecture (for new processing algorithms, assigned data)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\newpage
\part{Field analysis}
% (обзор литературы)
%Problem field (предметная область), concurrent solutions, connected works (смежные работы) etc

\section{Input data}
\subsection{Format}
%Maybe not very specific, just what data looks like.
\subsection{Error type classification and rates}
%For different sequencers and single cell or just for current state illumina???
\subsection{Does the read length matter or why is paired information so important}

\section{Typical assembler workflow}
\myignore{
\subsection{Error correction}
\subsection{Graph construction}
\subsection{Graph simplification}
\subsection{Repeat resolving}
\subsection{Scaffolding}
\subsection{Consensus step}
}

\section{Most popular existing assemblers (that work with double-barreled data) and their problems}

\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\part{Suggested solution (main part)}
\section{\dbg construction}
\section{Condensed \dbg that we work with (implicit reverse complement info consistensy maintaining)}
\section{Condensed graph construction}
%todo maybe move to implementation part???
\section{Graph operations}

\section{Associated information}
\subsection{Coverage}
\subsubsection{Why do we need it}
\subsubsection{Calculation variants}
\subsubsection{Transformation rules}

%todo make section
\subsection{Paired edges information}
\subsubsection{Why do we need it}
\subsubsection{Calculation variants}
\subsubsection{Online clustering}
\subsubsection{Transformation rules}
\subsubsection{Offline clustering}
\subsubsection{Information adjustment}

\subsection{Alternative strategies for associated info maintaining}
%todo check who does this
\subsubsection{Read paths maintaining (transformation on every operation still needed)}
\subsubsection{Intellectual read threading}
\subsubsection{History (futher detalization needed), useful not only for this}

\newpage

\section{Graph simplification}
\subsection{Why do we need this second error correction step}
\subsection{Classification of erroneous edges}
\subsection{Why do we need generic context free procedures (coverage needed anyway)}
\subsection{Simple tips clipping}
\subsubsection{Generic context free algorithm}
\subsubsection{Additional conditions based on paired info and sequences}
\subsection{Simple bulges removal}
\subsubsection{Generic context free algorithm}
\subsubsection{True edge deletion and error corruption strategy}
\subsubsection{Additional conditions based on paired info and sequences}
\subsection{Erroneous connections removal}

\section{Two words about repeat resolving}

\part{Architecture, implementation features}
\section{Utility structures}
\section{Uncondensed graph implementation}
\section{Condensed graph implementation}
\section{Concept of listeners and correct sequence of event firing}
\section{Smart iterators}
\section{Processing algorithms interfaces}

%Architecture, main troubles etc
\newpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\part{Experimental results}
\section{Comparison of different maps for k-mer storage}
\section{Performance, main bottlenecks}
\section{Comparison with Velvet}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\part{Conclusions}
\section{Work results}
\section{Future work}

%%%%%%%%%random
\myignore{
Why paired info is so important?? Read length is important to resolve repeats (obvious theoretical bound), often paired read acts as effectively much much longer read! (example on how can we use paired info).

How do we use paired info?
}
\end{document}
